Method for modulating plant growth, nucleic acid molecules and polypeptides encoded thereof useful as modulating agent

Abstract

The invention provides isolated nucleic acids molecules, designated CCP nucleic acid molecules, which encode novel cell cycle associated polypeptides. The invention also provides antisense nucleic acid molecules, recombinant expression vectors containing CCP nucleic acid molecules, host cells into which the expression vectors have been introduced, and transgenic plants in which a CCP gene has been introduced or disrupted. The invention still further provides isolated CCP proteins, fusion proteins, antigenic peptides and anti-CCP antibodies. Agricultural, diagnostic, screening, and therapeutic methods utilizing compositions of the invention are also provided.

1 . An isolated nucleic acid molecule selected from the group consisting of:
 (a) a nucleic acid molecule comprising the nucleotide sequence set forth in SEQ ID NO: 3, 6, 12, 13, 29, 41, 42, or 45;   (b) a nucleic acid molecule which encodes a polypeptide comprising the amino acid sequence set forth in SEQ ID NO: 69, 72, 78, 79, 95, 108, or 111;   (c) a nucleic acid molecule which encodes a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence set forth in SEQ ID NOs: 69, 72, 78, 79, 95, 108, or 111;   (d) a nucleic acid molecule comprising a nucleotide sequence which is at least 60% identical to the nucleotide sequence of SEQ ID NO: 3, 6, 12, 13, 29, 41, 42, or 45, or a complement thereof;   (e) a nucleic acid molecule comprising a fragment of at least 50 nucleotides of a nucleic acid comprising the nucleotide sequence of SEQ ID NO: 3, 6, 12, 13, 29, 41, 42, or 45, or a complement thereof;   (f) a nucleic acid molecule which encodes a polypeptide comprising an amino acid sequence at least about 60% identical to the amino acid sequence of SEQ ID NO: 69, 72, 78, 79, 95, 108, or 111; and   (g) a nucleic acid molecule which encodes a fragment of a polypeptide comprising the amino acid sequence of SEQ ID NO: 69, 72, 78, 79, 95, 108, or 111, wherein the fragment comprises at least 15 contiguous amino acid residues of the amino acid sequence of SEQ ID NO: 69, 72, 78, 79, 95, 108, or 111.   
     
     
         2 - 4 . (canceled) 
     
     
         5 . An isolated nucleic acid molecule which hybridizes to the nucleic acid molecule of  claim 1 , under stringent conditions. 
     
     
         6 . An isolated nucleic acid molecule comprising a nucleotide sequence which is complementary to the nucleotide sequence of the nucleic acid molecule of  claim 1 . 
     
     
         7 . An isolated nucleic acid molecule comprising the nucleic acid molecule of  claim 1 , and a nucleotide sequence encoding a heterologous peptide. 
     
     
         8 . A vector comprising the nucleic acid molecule of  claim 1 . 
     
     
         9 . A cell comprising the nucleic acid molecule of  claim 1 . 
     
     
         10 . A host cell transfected with the vector of  claim 8 . 
     
     
         11 . A method of producing a polypeptide comprising culturing the host cell of  claim 10  in an appropriate culture medium to, thereby, produce the polypeptide. 
     
     
         12 . An isolated polypeptide selected from the group consisting of:
 a) a fragment of a polypeptide comprising the amino acid sequence of SEQ ID NOs: 69, 72, 78, 79, 95, 108, or 11, wherein the fragment comprises at least 15 contiguous amino acids of SEQ ID NOs:69, 72, 78, 79, 95, 108, or 111;   b) a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ID NOs:69, 72, 78, 79, 95, 108, or 111, wherein the polypeptide is encoded by a nucleic acid molecule which hybridizes to a nucleic acid molecule consisting of SEQ ID NOs:3, 6, 12, 13, 29, 41, 42, or 45 under stringent conditions;   c) a polypeptide which is encoded by a nucleic acid molecule comprising a nucleotide sequence which is at least 60% identical to a nucleic acid comprising the nucleotide sequence of SEQ ID NOs:3, 6, 12, 13, 29, 41, 42, or 45; and   d) a polypeptide comprising an amino acid sequence which is at least 60% identical to the amino acid sequence of SEQ ID NOs:69, 72, 78, 79, 95, 108, or 111.   
     
     
         13 . The isolated polypeptide of  claim 12  comprising the amino acid sequence of SEQ ID NOs:69, 72, 78, 79, 95, 108, or 111. 
     
     
         14 . The polypeptide of  claim 12 , further comprising one or more heterologous amino acid sequences. 
     
     
         15 . An antibody which selectively binds to a polypeptide of  claim 12 . 
     
     
         16 . A method for detecting the presence of a polypeptide of  claim 12  in a sample comprising:
 a) contacting the sample with a compound which selectively binds to the polypeptide; and 
 b) determining whether the compound binds to the polypeptide in the sample to thereby detect the presence of a polypeptide of  claim 12  in the sample. 
 
     
     
         17 . The method of  claim 16 , wherein the compound which binds to the polypeptide is an antibody. 
     
     
         18 . A kit comprising a compound which selectively binds to a polypeptide of  claim 12  and instructions for use. 
     
     
         19 . A method for detecting the presence of the nucleic acid molecule of  claim 1  in a sample comprising:
 a) contacting the sample with a nucleic acid probe or primer which selectively hybridizes to the nucleic acid molecule; and 
 b) determining whether the nucleic acid probe or primer binds to a nucleic acid molecule in the sample to thereby detect the presence of nucleic acid molecule of  claim 1  in the sample. 
 
     
     
         20 . The method of  claim 19 , wherein the sample comprises mRNA molecules and is contacted with a nucleic acid probe. 
     
     
         21 . A kit comprising a compound which selectively hybridizes to a nucleic acid molecule of  claim 1  and instructions for use. 
     
     
         22 . A method for identifying a compound which binds to the polypeptide of  claim 12  comprising:
 a) contacting the polypeptide, or a cell expressing the polypeptide with a test compound; and 
 b) determining whether the polypeptide binds to the test compound. 
 
     
     
         23 . The method of  claim 22 , wherein the binding of the test compound to the polypeptide is detected by a method selected from the group consisting of:
 a) detection of binding by direct detection of test compound/polypeptide binding;   b) detection of binding using a competition binding assay; and   c) detection of binding using an assay for CCP activity.   
     
     
         24 . A method for modulating the activity of a polypeptide of  claim 12  comprising contacting the polypeptide or a cell expressing the polypeptide with a compound which binds to the polypeptide in a sufficient concentration to modulate the activity of the polypeptide. 
     
     
         25 . A method for identifying a compound which modulates the activity of a polypeptide of  claim 12  comprising:
 a) contacting a polypeptide of  claim 12  with a test compound; and 
 b) determining the effect of the test compound on the activity of the polypeptide to thereby identify a compound which modulates the activity of the polypeptide. 
 
     
     
         26 . A transgenic plant comprising the nucleic acid molecule of  claim 1 . 
     
     
         27 . The transgenic plant of  claim 26 , wherein the plant is a monocot plant. 
     
     
         28 . The transgenic plant of  claim 26 , wherein the plant is a dicot plant. 
     
     
         29 . The transgenic plant of  claim 26 , wherein the plant is selected from the group consisting of  Arabidopsis thaliana , rice, wheat, maize, tomato, oilseed rape, soybean, sunflower, and canola. 
     
     
         30 . A method for modulating the growth of a plant, comprising introducing into the plant a CCP modulator in an amount sufficient to modulate the growth of the plant, thereby modulating the growth of the plant. 
     
     
         31 . The method of  claim 30 , wherein the CCP modulator is a small molecule. 
     
     
         32 . The method of  claim 30 , wherein the CCP modulator is capable of modulating CCP polypeptide activity. 
     
     
         33 . The method of  claim 32 , wherein the CCP modulator is an anti-CCP antibody; or
 wherein the CCP modulator is a CCP polypeptide comprising the amino acid sequence of SEQ ID NOs: 67-132, 205, 211, 215-216 or 220-227, or a fragment thereof.   
     
     
         34 . (canceled) 
     
     
         35 . The method of  claim 30 , wherein the CCP modulator is capable of modulating CCP nucleic acid expression. 
     
     
         36 . The method of  claim 35 , wherein the CCP modulator is an antisense CCP nucleic acid molecule; wherein the CCP modulator is a ribozyme; or wherein the CCP modulator comprises the nucleotide sequence of SEQ ID NO: 1-66 or 228-239, or a fragment thereof. 
     
     
         37 - 38 . (canceled) 
     
     
         39 . The method of  claim 30 , wherein the plant is a monocot plant. 
     
     
         40 . The method of  claim 30 , wherein the plant is a dicot plant. 
     
     
         41 . The method of  claim 30 , wherein the plant is selected from the group consisting of  Arabidopsis thaliana , rice, wheat, maize, tomato, alfalfa, oilseed rape, soybean, sunflower, and canola. 
     
     
         42 . A method for modulating the cell cycle in a plant, comprising introducing into the plant a CCP modulator in an amount sufficient to modulate the cell cycle in the plant, thereby modulating the cell cycle in the plant. 
     
     
         43 . The method of  claim 42 , wherein the plant is a monocot plant. 
     
     
         44 . The method of  claim 42 , wherein the plant is a dicot plant. 
     
     
         45 . The method of  claim 42 , wherein the plant is selected from the group consisting of  Arabidopsis thaliana , rice, wheat, maize, tomato, alfalfa, oilseed rape, soybean, sunflower, and canola